This repository contains a jupyter notebook tutorial together with the necessary information and code for estimating free energy landscapes with Gaussian mixture models and extracting core-states from density maxima with InfleCS clustering.
Dependencies:
- Python 3.6
- Scikit-learn 0.19 or later
- Matplotlib
Free energy estimation with Gaussian mixture models
Inference of Calmodulin’s Ca2+-Dependent Free Energy Landscapes via Gaussian Mixture Model Validation
Annie M. Westerlund, Tyler J. Harpole, Christian Blau, and Lucie Delemotte
Journal of Chemical Theory and Computation, 2018
DOI: 10.1021/acs.jctc.7b00346
Clustering with InfleCS
InfleCS: Clustering Free Energy Landscapes with Gaussian Mixtures
Annie M. Westerlund, Lucie Delemotte
Journal of Chemical Theory and Computation, 2019
DOI: 10.1021/acs.jctc.9b00454
Annie Westerlund, KTH Royal Institute of Technology, 2019